ID   UBP13_CHICK             Reviewed;         862 AA.
AC   E1BY77;
DT   13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT   02-NOV-2010, sequence version 1.
DT   27-MAR-2024, entry version 88.
DE   RecName: Full=Ubiquitin carboxyl-terminal hydrolase 13;
DE            EC=3.4.19.12;
DE   AltName: Full=Deubiquitinating enzyme 13;
DE   AltName: Full=Ubiquitin thioesterase 13;
DE   AltName: Full=Ubiquitin-specific-processing protease 13;
GN   Name=USP13;
OS   Gallus gallus (Chicken).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC   Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae;
OC   Phasianinae; Gallus.
OX   NCBI_TaxID=9031;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Red jungle fowl;
RX   PubMed=15592404; DOI=10.1038/nature03154;
RA   Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P.,
RA   Bork P., Burt D.W., Groenen M.A.M., Delany M.E., Dodgson J.B.,
RA   Chinwalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D., Fronick C.,
RA   Fulton R.S., Graves T.A., Kremitzki C., Layman D., Magrini V.,
RA   McPherson J.D., Miner T.L., Minx P., Nash W.E., Nhan M.N., Nelson J.O.,
RA   Oddy L.G., Pohl C.S., Randall-Maher J., Smith S.M., Wallis J.W.,
RA   Yang S.-P., Romanov M.N., Rondelli C.M., Paton B., Smith J., Morrice D.,
RA   Daniels L., Tempest H.G., Robertson L., Masabanda J.S., Griffin D.K.,
RA   Vignal A., Fillon V., Jacobbson L., Kerje S., Andersson L.,
RA   Crooijmans R.P., Aerts J., van der Poel J.J., Ellegren H., Caldwell R.B.,
RA   Hubbard S.J., Grafham D.V., Kierzek A.M., McLaren S.R., Overton I.M.,
RA   Arakawa H., Beattie K.J., Bezzubov Y., Boardman P.E., Bonfield J.K.,
RA   Croning M.D.R., Davies R.M., Francis M.D., Humphray S.J., Scott C.E.,
RA   Taylor R.G., Tickle C., Brown W.R.A., Rogers J., Buerstedde J.-M.,
RA   Wilson S.A., Stubbs L., Ovcharenko I., Gordon L., Lucas S., Miller M.M.,
RA   Inoko H., Shiina T., Kaufman J., Salomonsen J., Skjoedt K., Wong G.K.-S.,
RA   Wang J., Liu B., Wang J., Yu J., Yang H., Nefedov M., Koriabine M.,
RA   Dejong P.J., Goodstadt L., Webber C., Dickens N.J., Letunic I., Suyama M.,
RA   Torrents D., von Mering C., Zdobnov E.M., Makova K., Nekrutenko A.,
RA   Elnitski L., Eswara P., King D.C., Yang S.-P., Tyekucheva S.,
RA   Radakrishnan A., Harris R.S., Chiaromonte F., Taylor J., He J.,
RA   Rijnkels M., Griffiths-Jones S., Ureta-Vidal A., Hoffman M.M., Severin J.,
RA   Searle S.M.J., Law A.S., Speed D., Waddington D., Cheng Z., Tuzun E.,
RA   Eichler E., Bao Z., Flicek P., Shteynberg D.D., Brent M.R., Bye J.M.,
RA   Huckle E.J., Chatterji S., Dewey C., Pachter L., Kouranov A.,
RA   Mourelatos Z., Hatzigeorgiou A.G., Paterson A.H., Ivarie R., Brandstrom M.,
RA   Axelsson E., Backstrom N., Berlin S., Webster M.T., Pourquie O.,
RA   Reymond A., Ucla C., Antonarakis S.E., Long M., Emerson J.J., Betran E.,
RA   Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G., Furey T.S.,
RA   Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D., Eyras E.,
RA   Castelo R., Abril J.F., Castellano S., Camara F., Parra G., Guigo R.,
RA   Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A., Mardis E.R.,
RA   Wilson R.K.;
RT   "Sequence and comparative analysis of the chicken genome provide unique
RT   perspectives on vertebrate evolution.";
RL   Nature 432:695-716(2004).
CC   -!- FUNCTION: Deubiquitinase that mediates deubiquitination of target
CC       proteins and is involved in various processes such as autophagy and
CC       endoplasmic reticulum-associated degradation (ERAD).
CC       {ECO:0000250|UniProtKB:Q92995}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC         and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC         residue protein attached to proteins as an intracellular targeting
CC         signal).; EC=3.4.19.12;
CC   -!- ACTIVITY REGULATION: Specifically inhibited by spautin-1 (specific and
CC       potent autophagy inhibitor-1), a derivative of MBCQ that binds to USP13
CC       and inhibits deubiquitinase activity. {ECO:0000250}.
CC   -!- DOMAIN: The UBP-type zinc finger has lost its ability to bind ubiquitin
CC       and USP13 is not activated by unanchored ubiquitin. {ECO:0000250}.
CC   -!- DOMAIN: The UBA domains mediate binding to ubiquitin. {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR   EMBL; AADN02020803; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AADN02020804; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AADN02020805; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AADN02020806; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   AlphaFoldDB; E1BY77; -.
DR   SMR; E1BY77; -.
DR   STRING; 9031.ENSGALP00000014471; -.
DR   PaxDb; 9031-ENSGALP00000014471; -.
DR   Ensembl; ENSGALT00010043807.1; ENSGALP00010026057.1; ENSGALG00010018123.1.
DR   Ensembl; ENSGALT00015043551; ENSGALP00015025575; ENSGALG00015017774.
DR   VEuPathDB; HostDB:geneid_429286; -.
DR   eggNOG; KOG0944; Eukaryota.
DR   GeneTree; ENSGT00940000157401; -.
DR   HOGENOM; CLU_009884_1_0_1; -.
DR   InParanoid; E1BY77; -.
DR   OMA; ASTECAY; -.
DR   OrthoDB; 166948at2759; -.
DR   PhylomeDB; E1BY77; -.
DR   TreeFam; TF300576; -.
DR   Proteomes; UP000000539; Chromosome 9.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:1904288; F:BAT3 complex binding; IEA:Ensembl.
DR   GO; GO:0004843; F:cysteine-type deubiquitinase activity; ISS:UniProtKB.
DR   GO; GO:0004197; F:cysteine-type endopeptidase activity; ISS:UniProtKB.
DR   GO; GO:1990380; F:K48-linked deubiquitinase activity; IEA:Ensembl.
DR   GO; GO:0070628; F:proteasome binding; IEA:Ensembl.
DR   GO; GO:0051087; F:protein-folding chaperone binding; IEA:Ensembl.
DR   GO; GO:0043130; F:ubiquitin binding; ISS:UniProtKB.
DR   GO; GO:0031625; F:ubiquitin protein ligase binding; IEA:Ensembl.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR   GO; GO:0006914; P:autophagy; IEA:UniProtKB-KW.
DR   GO; GO:0008283; P:cell population proliferation; ISS:UniProtKB.
DR   GO; GO:0036506; P:maintenance of unfolded protein; IEA:Ensembl.
DR   GO; GO:1904294; P:positive regulation of ERAD pathway; IEA:Ensembl.
DR   GO; GO:0070536; P:protein K63-linked deubiquitination; ISS:UniProtKB.
DR   GO; GO:0050821; P:protein stabilization; ISS:UniProtKB.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   GO; GO:0010506; P:regulation of autophagy; ISS:UniProtKB.
DR   GO; GO:0006355; P:regulation of DNA-templated transcription; ISS:UniProtKB.
DR   CDD; cd02658; Peptidase_C19B; 1.
DR   CDD; cd14384; UBA1_UBP13; 1.
DR   CDD; cd14386; UBA2_UBP5; 1.
DR   Gene3D; 3.90.70.10; Cysteine proteinases; 2.
DR   Gene3D; 1.10.8.10; DNA helicase RuvA subunit, C-terminal domain; 2.
DR   Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 2.
DR   InterPro; IPR038765; Papain-like_cys_pep_sf.
DR   InterPro; IPR001394; Peptidase_C19_UCH.
DR   InterPro; IPR015940; UBA.
DR   InterPro; IPR009060; UBA-like_sf.
DR   InterPro; IPR016652; Ubiquitinyl_hydrolase.
DR   InterPro; IPR041432; UBP13_Znf-UBP_var.
DR   InterPro; IPR018200; USP_CS.
DR   InterPro; IPR028889; USP_dom.
DR   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   InterPro; IPR001607; Znf_UBP.
DR   PANTHER; PTHR21646; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR   PANTHER; PTHR21646:SF10; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 14; 1.
DR   Pfam; PF00627; UBA; 2.
DR   Pfam; PF00443; UCH; 1.
DR   Pfam; PF02148; zf-UBP; 1.
DR   Pfam; PF17807; zf-UBP_var; 1.
DR   PIRSF; PIRSF016308; UBP; 1.
DR   SMART; SM00165; UBA; 2.
DR   SMART; SM00290; ZnF_UBP; 1.
DR   SUPFAM; SSF54001; Cysteine proteinases; 1.
DR   SUPFAM; SSF57850; RING/U-box; 1.
DR   SUPFAM; SSF46934; UBA-like; 1.
DR   PROSITE; PS50030; UBA; 2.
DR   PROSITE; PS00972; USP_1; 1.
DR   PROSITE; PS00973; USP_2; 1.
DR   PROSITE; PS50235; USP_3; 1.
DR   PROSITE; PS50271; ZF_UBP; 1.
PE   3: Inferred from homology;
KW   Autophagy; Hydrolase; Metal-binding; Protease; Reference proteome; Repeat;
KW   Thiol protease; Ubl conjugation pathway; Zinc; Zinc-finger.
FT   CHAIN           1..862
FT                   /note="Ubiquitin carboxyl-terminal hydrolase 13"
FT                   /id="PRO_0000418012"
FT   DOMAIN          331..860
FT                   /note="USP"
FT   DOMAIN          647..688
FT                   /note="UBA 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT   DOMAIN          722..762
FT                   /note="UBA 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT   ZN_FING         182..290
FT                   /note="UBP-type; degenerate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   ACT_SITE        340
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   ACT_SITE        822
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   BINDING         206
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         209
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         226
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT   BINDING         239
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
SQ   SEQUENCE   862 AA;  96649 MW;  9207A3B6846A1018 CRC64;
     MQRAALFGGG DAQMAAGDLG ELLVPYMPTI RVPKSGDRVY KTECAFSYDS PDSEGGLYVC
     MNTFLGFGRE HIERHYRKTG QCVYLHLKRH VIEKVPGASG GALPKRRNAK LFLDLEANGD
     LSSDDFEYED EAKLVIFPDH YEISLPNIEE LPALVTIASD ALLSAKSPYR KQDPDSWEEE
     LQASKHAKSL VQLDNGVRIP PSGWKCSKCD LRENLWLNLT DGSVLCGKWF FDGSGGNGHA
     MEHYKETGYP LAVKLGTITP DGADVYSFDE EEPVLDPHIA KHLAHFGIDM LQMQVAENGL
     RDNDIKPRVS EWEVIQEAGV KLKPMYGPGY TGMKNLGNSC YLNAVMQAIF SIPEFQRAYV
     GNLPRIFDYS PLDPTQDFNT QMAKLGHGLL SGQYSKPPMK SELIEQVMKE EHKPQQNGIS
     PQMFKAFISK DHTEFSSNRQ QDAQEFFLHL INLVERNPVG SENPSDVFRF LVEERTQCCQ
     SRKVRYTERV DYIMQLPVAM EAATNKDELI AYELKRREAE AARRAPPELV RAKIPFSACL
     QAFSEPTNVE DFWSSALQAK SAGVKTSRFA SFPQYLVVQI KKFTFGLDWI PKKLDVSIDM
     PDFLDISHLR AMGLQPGEEE LPDIAPPIII PEDPKDRMMN NFVESLDIDE SSVMQLAEMG
     FPLEACRKAV YYTGNLGAEV AFNWIIAHME EPDFAEPLVV PVFGGAASSG VAGLGAVGLD
     NQPPEEMVSI IISMGFQRSL AIQALKATNN NLERALEWIF SHPELEEEDG EPALNVMDLE
     NHTNANILAE ARSEGPRIKD GPGRYELFGF ISHMGTSTMS GHYVCHLKKE GRWVIYNDLR
     VCASERPPKD LGYIYFYHRI PS
//